| 1 | /* -*- mode: c++; c-basic-offset: 4; indent-tabs-mode: nil -*- */ |
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| 2 | /* |
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| 3 | * ---------------------------------------------------------------------- |
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| 4 | * Nanovis: Visualization of Nanoelectronics Data |
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| 5 | * |
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| 6 | * dxReader.cpp |
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| 7 | * This module contains openDX readers for 2D and 3D volumes. |
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| 8 | * |
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| 9 | * ====================================================================== |
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| 10 | * AUTHOR: Wei Qiao <qiaow@purdue.edu> |
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| 11 | * Michael McLennan <mmclennan@purdue.edu> |
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| 12 | * Purdue Rendering and Perceptualization Lab (PURPL) |
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| 13 | * |
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| 14 | * Copyright (c) 2004-2013 HUBzero Foundation, LLC |
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| 15 | * |
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| 16 | * See the file "license.terms" for information on usage and |
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| 17 | * redistribution of this file, and for a DISCLAIMER OF ALL WARRANTIES. |
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| 18 | * ====================================================================== |
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| 19 | */ |
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| 20 | #include <stdio.h> |
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| 21 | #include <math.h> |
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| 22 | #include <sys/types.h> |
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| 23 | #include <unistd.h> |
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| 24 | #include <float.h> |
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| 25 | |
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| 26 | #include <fstream> |
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| 27 | #include <iostream> |
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| 28 | #include <sstream> |
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| 29 | #include <string> |
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| 30 | |
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| 31 | #include <RpOutcome.h> |
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| 32 | #include <RpField1D.h> |
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| 33 | #include <RpFieldRect3D.h> |
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| 34 | #include <RpFieldPrism3D.h> |
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| 35 | |
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| 36 | // common file/data reader functions |
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| 37 | #include "ReaderCommon.h" |
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| 38 | |
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| 39 | #include "config.h" |
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| 40 | #include "nanovis.h" |
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| 41 | #include "Unirect.h" |
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| 42 | #include "Volume.h" |
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| 43 | #include "ZincBlendeVolume.h" |
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| 44 | #include "NvZincBlendeReconstructor.h" |
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| 45 | |
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| 46 | /** |
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| 47 | * \brief Load a 3D volume from a dx-format file |
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| 48 | * |
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| 49 | * In DX format: |
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| 50 | * rank 0 means scalars, |
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| 51 | * rank 1 means vectors, |
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| 52 | * rank 2 means matrices, |
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| 53 | * rank 3 means tensors |
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| 54 | * |
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| 55 | * For rank 1, shape is a single number equal to the number of dimensions. |
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| 56 | * e.g. rank 1 shape 3 means a 3-component vector field |
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| 57 | */ |
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| 58 | Volume * |
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| 59 | load_dx_volume_stream(Rappture::Outcome& result, const char *tag, |
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| 60 | std::iostream& fin) |
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| 61 | { |
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| 62 | TRACE("Enter tag:%s", tag); |
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| 63 | |
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| 64 | Rappture::MeshTri2D xymesh; |
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| 65 | int dummy, nx, ny, nz, nxy, npts; |
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| 66 | // origin |
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| 67 | double x0, y0, z0; |
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| 68 | // deltas (cell dimensions) |
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| 69 | double dx, dy, dz; |
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| 70 | // length of volume edges |
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| 71 | double lx, ly, lz; |
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| 72 | // temps for delta values |
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| 73 | double ddx, ddy, ddz; |
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| 74 | char line[128], type[128], *start; |
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| 75 | |
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| 76 | int isrect = 1; |
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| 77 | |
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| 78 | dx = dy = dz = 0.0; |
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| 79 | x0 = y0 = z0 = 0.0; // May not have an origin line. |
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| 80 | nx = ny = nz = npts = nxy = 0; |
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| 81 | while (!fin.eof()) { |
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| 82 | fin.getline(line, sizeof(line) - 1); |
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| 83 | if (fin.fail()) { |
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| 84 | result.error("error in data stream"); |
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| 85 | return NULL; |
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| 86 | } |
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| 87 | for (start = line; *start == ' ' || *start == '\t'; start++) |
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| 88 | ; // skip leading blanks |
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| 89 | |
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| 90 | if (*start != '#') { // skip comment lines |
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| 91 | if (sscanf(start, "object %d class gridpositions counts %d %d %d", |
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| 92 | &dummy, &nx, &ny, &nz) == 4) { |
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| 93 | // found grid size |
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| 94 | isrect = 1; |
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| 95 | } else if (sscanf(start, "object %d class array type float rank 1 shape 3 items %d data follows", |
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| 96 | &dummy, &nxy) == 2) { |
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| 97 | isrect = 0; |
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| 98 | |
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| 99 | double xx, yy, zz; |
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| 100 | for (int i = 0; i < nxy; i++) { |
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| 101 | fin.getline(line,sizeof(line)-1); |
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| 102 | if (sscanf(line, "%lg %lg %lg", &xx, &yy, &zz) == 3) { |
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| 103 | xymesh.addNode(Rappture::Node2D(xx, yy)); |
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| 104 | } |
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| 105 | } |
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| 106 | |
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| 107 | char fpts[128]; |
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| 108 | sprintf(fpts, "/tmp/tmppts%d", getpid()); |
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| 109 | char fcells[128]; |
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| 110 | sprintf(fcells, "/tmp/tmpcells%d", getpid()); |
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| 111 | |
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| 112 | std::ofstream ftmp(fpts); |
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| 113 | // save corners of bounding box first, to work around meshing |
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| 114 | // problems in voronoi utility |
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| 115 | int numBoundaryPoints = 4; |
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| 116 | |
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| 117 | // Bump out the bounds by an epsilon to avoid problem when |
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| 118 | // corner points are already nodes |
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| 119 | double XEPS = (xymesh.rangeMax(Rappture::xaxis) - |
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| 120 | xymesh.rangeMin(Rappture::xaxis)) / 10.0f; |
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| 121 | |
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| 122 | double YEPS = (xymesh.rangeMax(Rappture::yaxis) - |
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| 123 | xymesh.rangeMin(Rappture::yaxis)) / 10.0f; |
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| 124 | |
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| 125 | ftmp << xymesh.rangeMin(Rappture::xaxis) - XEPS << " " |
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| 126 | << xymesh.rangeMin(Rappture::yaxis) - YEPS << std::endl; |
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| 127 | ftmp << xymesh.rangeMax(Rappture::xaxis) + XEPS << " " |
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| 128 | << xymesh.rangeMin(Rappture::yaxis) - YEPS << std::endl; |
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| 129 | ftmp << xymesh.rangeMax(Rappture::xaxis) + XEPS << " " |
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| 130 | << xymesh.rangeMax(Rappture::yaxis) + YEPS << std::endl; |
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| 131 | ftmp << xymesh.rangeMin(Rappture::xaxis) - XEPS << " " |
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| 132 | << xymesh.rangeMax(Rappture::yaxis) + YEPS << std::endl; |
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| 133 | |
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| 134 | for (int i = 0; i < nxy; i++) { |
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| 135 | ftmp << xymesh.atNode(i).x() << " " << xymesh.atNode(i).y() << std::endl; |
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| 136 | } |
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| 137 | ftmp.close(); |
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| 138 | |
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| 139 | char cmdstr[512]; |
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| 140 | sprintf(cmdstr, "voronoi -t < %s > %s", fpts, fcells); |
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| 141 | if (system(cmdstr) == 0) { |
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| 142 | int cx, cy, cz; |
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| 143 | std::ifstream ftri(fcells); |
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| 144 | while (!ftri.eof()) { |
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| 145 | ftri.getline(line,sizeof(line)-1); |
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| 146 | if (sscanf(line, "%d %d %d", &cx, &cy, &cz) == 3) { |
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| 147 | if (cx >= numBoundaryPoints && |
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| 148 | cy >= numBoundaryPoints && |
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| 149 | cz >= numBoundaryPoints) { |
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| 150 | // skip boundary points we added |
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| 151 | xymesh.addCell(cx - numBoundaryPoints, |
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| 152 | cy - numBoundaryPoints, |
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| 153 | cz - numBoundaryPoints); |
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| 154 | } |
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| 155 | } |
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| 156 | } |
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| 157 | ftri.close(); |
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| 158 | } else { |
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| 159 | result.error("triangularization failed"); |
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| 160 | return NULL; |
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| 161 | } |
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| 162 | unlink(fpts); |
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| 163 | unlink(fcells); |
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| 164 | } else if (sscanf(start, "object %d class regulararray count %d", &dummy, &nz) == 2) { |
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| 165 | // found z-grid |
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| 166 | } else if (sscanf(start, "origin %lg %lg %lg", &x0, &y0, &z0) == 3) { |
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| 167 | // found origin |
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| 168 | } else if (sscanf(start, "delta %lg %lg %lg", &ddx, &ddy, &ddz) == 3) { |
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| 169 | // found one of the delta lines |
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| 170 | int count = 0; |
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| 171 | if (ddx != 0.0) { |
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| 172 | dx = ddx; |
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| 173 | count++; |
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| 174 | } |
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| 175 | if (ddy != 0.0) { |
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| 176 | dy = ddy; |
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| 177 | count++; |
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| 178 | } |
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| 179 | if (ddz != 0.0) { |
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| 180 | dz = ddz; |
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| 181 | count++; |
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| 182 | } |
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| 183 | if (count > 1) { |
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| 184 | result.addError("don't know how to handle multiple non-zero" |
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| 185 | " delta values"); |
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| 186 | return NULL; |
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| 187 | } |
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| 188 | } else if (sscanf(start, "object %d class array type %s rank 0 items %d data follows", |
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| 189 | &dummy, type, &npts) == 3) { |
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| 190 | if (isrect && (npts != nx*ny*nz)) { |
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| 191 | result.addError("inconsistent data: expected %d points" |
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| 192 | " but found %d points", nx*ny*nz, npts); |
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| 193 | return NULL; |
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| 194 | } else if (!isrect && (npts != nxy*nz)) { |
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| 195 | result.addError("inconsistent data: expected %d points" |
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| 196 | " but found %d points", nxy*nz, npts); |
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| 197 | return NULL; |
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| 198 | } |
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| 199 | break; |
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| 200 | } else if (sscanf(start, "object %d class array type %s rank 0 times %d data follows", |
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| 201 | &dummy, type, &npts) == 3) { |
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| 202 | if (npts != nx*ny*nz) { |
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| 203 | result.addError("inconsistent data: expected %d points" |
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| 204 | " but found %d points", nx*ny*nz, npts); |
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| 205 | return NULL; |
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| 206 | } |
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| 207 | break; |
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| 208 | } |
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| 209 | } |
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| 210 | } |
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| 211 | |
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| 212 | TRACE("found nx=%d ny=%d nxy=%d nz=%d\ndx=%g dy=%g dz=%g\nx0=%g y0=%g z0=%g", |
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| 213 | nx, ny, nxy, nz, dx, dy, dz, x0, y0, z0); |
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| 214 | |
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| 215 | lx = (nx - 1) * dx; |
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| 216 | ly = (ny - 1) * dy; |
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| 217 | lz = (nz - 1) * dz; |
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| 218 | |
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| 219 | // read data points |
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| 220 | if (fin.eof()) { |
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| 221 | result.error("data not found in stream"); |
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| 222 | return NULL; |
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| 223 | } |
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| 224 | Volume *volume = NULL; |
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| 225 | float *data = NULL; |
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| 226 | double vmin = DBL_MAX; |
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| 227 | double nzero_min = DBL_MAX; |
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| 228 | double vmax = -DBL_MAX; |
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| 229 | if (isrect) { |
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| 230 | #ifdef DOWNSAMPLE_DATA |
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| 231 | Rappture::Mesh1D xgrid(x0, x0 + lx, nx); |
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| 232 | Rappture::Mesh1D ygrid(y0, y0 + ly, ny); |
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| 233 | Rappture::Mesh1D zgrid(z0, z0 + lz, nz); |
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| 234 | Rappture::FieldRect3D field(xgrid, ygrid, zgrid); |
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| 235 | #else // !DOWNSAMPLE_DATA |
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| 236 | data = new float[nx * ny * nz * 4]; |
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| 237 | memset(data, 0, nx*ny*nz*4); |
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| 238 | #endif // DOWNSAMPLE_DATA |
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| 239 | double dval[6]; |
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| 240 | int nread = 0; |
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| 241 | int ix = 0; |
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| 242 | int iy = 0; |
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| 243 | int iz = 0; |
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| 244 | |
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| 245 | while (!fin.eof() && nread < npts) { |
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| 246 | fin.getline(line,sizeof(line)-1); |
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| 247 | if (fin.fail()) { |
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| 248 | result.addError("error reading data points"); |
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| 249 | return NULL; |
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| 250 | } |
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| 251 | int n = sscanf(line, "%lg %lg %lg %lg %lg %lg", |
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| 252 | &dval[0], &dval[1], &dval[2], &dval[3], &dval[4], &dval[5]); |
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| 253 | for (int p = 0; p < n; p++) { |
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| 254 | #ifdef notdef |
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| 255 | if (isnan(dval[p])) { |
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| 256 | TRACE("Found NAN in input at %d,%d,%d", ix, iy, iz); |
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| 257 | } |
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| 258 | #endif |
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| 259 | #ifdef DOWNSAMPLE_DATA |
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| 260 | int nindex = iz*nx*ny + iy*nx + ix; |
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| 261 | field.define(nindex, dval[p]); |
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| 262 | #else // !DOWNSAMPLE_DATA |
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| 263 | int nindex = (iz*nx*ny + iy*nx + ix) * 4; |
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| 264 | data[nindex] = dval[p]; |
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| 265 | |
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| 266 | if (dval[p] < vmin) { |
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| 267 | vmin = dval[p]; |
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| 268 | } else if (dval[p] > vmax) { |
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| 269 | vmax = dval[p]; |
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| 270 | } |
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| 271 | if (dval[p] != 0.0 && dval[p] < nzero_min) { |
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| 272 | nzero_min = dval[p]; |
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| 273 | } |
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| 274 | #endif // DOWNSAMPLE_DATA |
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| 275 | nread++; |
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| 276 | if (++iz >= nz) { |
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| 277 | iz = 0; |
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| 278 | if (++iy >= ny) { |
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| 279 | iy = 0; |
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| 280 | ++ix; |
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| 281 | } |
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| 282 | } |
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| 283 | } |
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| 284 | } |
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| 285 | |
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| 286 | // make sure that we read all of the expected points |
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| 287 | if (nread != npts) { |
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| 288 | result.addError("inconsistent data: expected %d points" |
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| 289 | " but found %d points", npts, nread); |
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| 290 | return NULL; |
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| 291 | } |
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| 292 | |
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| 293 | #ifndef DOWNSAMPLE_DATA |
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| 294 | |
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| 295 | // scale all values [0-1], -1 => out of bounds |
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| 296 | normalizeScalar(data, npts, 4, vmin, vmax); |
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| 297 | computeSimpleGradient(data, nx, ny, nz, |
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| 298 | dx, dy, dz); |
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| 299 | #else // DOWNSAMPLE_DATA |
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| 300 | // figure out a good mesh spacing |
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| 301 | int nsample = 64; |
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| 302 | double dmin = pow((lx*ly*lz)/((nsample-1)*(nsample-1)*(nsample-1)), 0.333); |
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| 303 | |
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| 304 | nx = (int)ceil(lx/dmin) + 1; |
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| 305 | ny = (int)ceil(ly/dmin) + 1; |
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| 306 | nz = (int)ceil(lz/dmin) + 1; |
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| 307 | |
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| 308 | #ifndef HAVE_NPOT_TEXTURES |
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| 309 | // must be an even power of 2 for older cards |
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| 310 | nx = (int)pow(2.0, ceil(log10((double)nx)/log10(2.0))); |
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| 311 | ny = (int)pow(2.0, ceil(log10((double)ny)/log10(2.0))); |
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| 312 | nz = (int)pow(2.0, ceil(log10((double)nz)/log10(2.0))); |
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| 313 | #endif |
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| 314 | |
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| 315 | dx = lx /(double)(nx - 1); |
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| 316 | dy = ly /(double)(ny - 1); |
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| 317 | dz = lz /(double)(nz - 1); |
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| 318 | |
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| 319 | vmin = field.valueMin(); |
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| 320 | vmax = field.valueMax(); |
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| 321 | nzero_min = DBL_MAX; |
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| 322 | double dv = vmax - vmin; |
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| 323 | if (dv == 0.0) { |
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| 324 | dv = 1.0; |
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| 325 | } |
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| 326 | |
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| 327 | int ngen = 0; |
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| 328 | #ifdef FILTER_GRADIENTS |
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| 329 | // Sobel filter expects a single float at |
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| 330 | // each node |
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| 331 | const int step = 1; |
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| 332 | float *cdata = new float[nx*ny*nz * step]; |
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| 333 | #else // !FILTER_GRADIENTS |
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| 334 | // Leave 3 floats of space for gradients |
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| 335 | // to be filled in by computeSimpleGradient() |
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| 336 | const int step = 4; |
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| 337 | data = new float[nx*ny*nz * step]; |
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| 338 | #endif // FILTER_GRADIENTS |
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| 339 | |
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| 340 | for (int iz = 0; iz < nz; iz++) { |
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| 341 | double zval = z0 + iz*dz; |
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| 342 | for (int iy = 0; iy < ny; iy++) { |
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| 343 | double yval = y0 + iy*dy; |
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| 344 | for (int ix = 0; ix < nx; ix++) { |
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| 345 | double xval = x0 + ix*dx; |
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| 346 | double v = field.value(xval, yval, zval); |
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| 347 | #ifdef notdef |
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| 348 | if (isnan(v)) { |
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| 349 | TRACE("NAN at %d,%d,%d: (%g, %g, %g)", ix, iy, iz, xval, yval, zval); |
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| 350 | } |
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| 351 | #endif |
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| 352 | if (v != 0.0 && v < nzero_min) { |
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| 353 | nzero_min = v; |
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| 354 | } |
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| 355 | #ifdef FILTER_GRADIENTS |
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| 356 | // NOT normalized, may have NaNs (FIXME: how does gradient filter handle NaN?) |
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| 357 | cdata[ngen] = v; |
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| 358 | #else // !FILTER_GRADIENTS |
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| 359 | // scale all values [0-1], -1 => out of bounds |
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| 360 | v = (isnan(v)) ? -1.0 : (v - vmin)/dv; |
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| 361 | data[ngen] = v; |
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| 362 | #endif // FILTER_GRADIENTS |
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| 363 | ngen += step; |
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| 364 | } |
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| 365 | } |
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| 366 | } |
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| 367 | #ifdef FILTER_GRADIENTS |
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| 368 | // computeGradient returns a new array with gradients |
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| 369 | // filled in, so data is now 4 floats per node |
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| 370 | data = computeGradient(cdata, nx, ny, nz, |
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| 371 | dx, dy, dz, |
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| 372 | vmin, vmax); |
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| 373 | delete [] cdata; |
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| 374 | #else // !FILTER_GRADIENTS |
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| 375 | computeSimpleGradient(data, nx, ny, nz, |
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| 376 | dx, dy, dz); |
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| 377 | #endif // FILTER_GRADIENTS |
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| 378 | |
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| 379 | #endif // DOWNSAMPLE_DATA |
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| 380 | } else { |
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| 381 | Rappture::Mesh1D zgrid(z0, z0 + (nz-1)*dz, nz); |
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| 382 | Rappture::FieldPrism3D field(xymesh, zgrid); |
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| 383 | |
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| 384 | double dval; |
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| 385 | int nread = 0; |
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| 386 | int ixy = 0; |
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| 387 | int iz = 0; |
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| 388 | while (!fin.eof() && nread < npts) { |
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| 389 | fin >> dval; |
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| 390 | if (fin.fail()) { |
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| 391 | result.addError("after %d of %d points: can't read number", |
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| 392 | nread, npts); |
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| 393 | return NULL; |
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| 394 | } else { |
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| 395 | int nid = nxy*iz + ixy; |
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| 396 | field.define(nid, dval); |
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| 397 | |
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| 398 | nread++; |
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| 399 | if (++iz >= nz) { |
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| 400 | iz = 0; |
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| 401 | ixy++; |
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| 402 | } |
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| 403 | } |
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| 404 | } |
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| 405 | |
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| 406 | // make sure that we read all of the expected points |
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| 407 | if (nread != npts) { |
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| 408 | result.addError("inconsistent data: expected %d points" |
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| 409 | " but found %d points", npts, nread); |
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| 410 | return NULL; |
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| 411 | } |
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| 412 | |
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| 413 | x0 = field.rangeMin(Rappture::xaxis); |
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| 414 | lx = field.rangeMax(Rappture::xaxis) - field.rangeMin(Rappture::xaxis); |
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| 415 | y0 = field.rangeMin(Rappture::yaxis); |
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| 416 | ly = field.rangeMax(Rappture::yaxis) - field.rangeMin(Rappture::yaxis); |
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| 417 | z0 = field.rangeMin(Rappture::zaxis); |
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| 418 | lz = field.rangeMax(Rappture::zaxis) - field.rangeMin(Rappture::zaxis); |
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| 419 | |
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| 420 | // figure out a good mesh spacing |
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| 421 | int nsample = 64; |
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| 422 | double dmin = pow((lx*ly*lz)/((nsample-1)*(nsample-1)*(nsample-1)), 0.333); |
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| 423 | |
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| 424 | nx = (int)ceil(lx/dmin) + 1; |
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| 425 | ny = (int)ceil(ly/dmin) + 1; |
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| 426 | nz = (int)ceil(lz/dmin) + 1; |
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| 427 | #ifndef HAVE_NPOT_TEXTURES |
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| 428 | // must be an even power of 2 for older cards |
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| 429 | nx = (int)pow(2.0, ceil(log10((double)nx)/log10(2.0))); |
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| 430 | ny = (int)pow(2.0, ceil(log10((double)ny)/log10(2.0))); |
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| 431 | nz = (int)pow(2.0, ceil(log10((double)nz)/log10(2.0))); |
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| 432 | #endif |
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| 433 | |
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| 434 | dx = lx /(double)(nx - 1); |
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| 435 | dy = ly /(double)(ny - 1); |
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| 436 | dz = lz /(double)(nz - 1); |
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| 437 | |
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| 438 | vmin = field.valueMin(); |
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| 439 | vmax = field.valueMax(); |
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| 440 | nzero_min = DBL_MAX; |
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| 441 | double dv = vmax - vmin; |
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| 442 | if (dv == 0.0) { |
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| 443 | dv = 1.0; |
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| 444 | } |
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| 445 | |
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| 446 | data = new float[4*nx*ny*nz]; |
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| 447 | // generate the uniformly sampled data that we need for a volume |
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| 448 | int ngen = 0; |
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| 449 | for (int iz = 0; iz < nz; iz++) { |
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| 450 | double zval = z0 + iz*dz; |
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| 451 | for (int iy = 0; iy < ny; iy++) { |
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| 452 | double yval = y0 + iy*dy; |
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| 453 | for (int ix = 0; ix < nx; ix++) { |
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| 454 | double xval = x0 + ix*dx; |
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| 455 | double v = field.value(xval, yval, zval); |
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| 456 | |
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| 457 | if (v != 0.0 && v < nzero_min) { |
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| 458 | nzero_min = v; |
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| 459 | } |
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| 460 | // scale all values [0-1], -1 => out of bounds |
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| 461 | v = (isnan(v)) ? -1.0 : (v - vmin)/dv; |
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| 462 | data[ngen] = v; |
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| 463 | |
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| 464 | ngen += 4; |
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| 465 | } |
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| 466 | } |
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| 467 | } |
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| 468 | |
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| 469 | computeSimpleGradient(data, nx, ny, nz, |
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| 470 | dx, dy, dz); |
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| 471 | } |
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| 472 | |
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| 473 | TRACE("nx = %i ny = %i nz = %i", nx, ny, nz); |
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| 474 | TRACE("x0 = %lg y0 = %lg z0 = %lg", x0, y0, z0); |
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| 475 | TRACE("lx = %lg ly = %lg lz = %lg", lx, ly, lz); |
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| 476 | TRACE("dx = %lg dy = %lg dz = %lg", dx, dy, dz); |
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| 477 | TRACE("dataMin = %lg dataMax = %lg nzero_min = %lg", |
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| 478 | vmin, vmax, nzero_min); |
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| 479 | |
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| 480 | volume = NanoVis::loadVolume(tag, nx, ny, nz, 4, data, |
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| 481 | vmin, vmax, nzero_min); |
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| 482 | volume->xAxis.setRange(x0, x0 + lx); |
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| 483 | volume->yAxis.setRange(y0, y0 + ly); |
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| 484 | volume->zAxis.setRange(z0, z0 + lz); |
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| 485 | volume->updatePending = true; |
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| 486 | |
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| 487 | delete [] data; |
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| 488 | |
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| 489 | // |
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| 490 | // Center this new volume on the origin. |
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| 491 | // |
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| 492 | float dx0 = -0.5; |
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| 493 | float dy0 = -0.5*ly/lx; |
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| 494 | float dz0 = -0.5*lz/lx; |
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| 495 | if (volume) { |
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| 496 | volume->location(vrmath::Vector3f(dx0, dy0, dz0)); |
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| 497 | TRACE("Set volume location to %g %g %g", dx0, dy0, dz0); |
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| 498 | } |
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| 499 | return volume; |
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| 500 | } |
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